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annotate Applications/DicomToTiff.cpp @ 169:de783db2a7c3

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making fix for issue #139 permanent
author Sebastien Jodogne <s.jodogne@gmail.com>
date Fri, 12 Jul 2019 12:53:26 +0200
parents 605247fc8758
children e3cbf890b588
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
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3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
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4 * Department, University Hospital of Liege, Belgium
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6b8ccfc02051 preparing for 2019
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5 * Copyright (C) 2017-2019 Osimis S.A., Belgium
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6 *
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7 * This program is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU Affero General Public License
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9 * as published by the Free Software Foundation, either version 3 of
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10 * the License, or (at your option) any later version.
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11 *
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12 * This program is distributed in the hope that it will be useful, but
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13 * WITHOUT ANY WARRANTY; without even the implied warranty of
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14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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15 * Affero General Public License for more details.
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16 *
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17 * You should have received a copy of the GNU Affero General Public License
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18 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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19 **/
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21
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22 #include "../Framework/DicomToolbox.h"
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23 #include "../Framework/ImageToolbox.h"
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24 #include "../Framework/Inputs/DicomPyramid.h"
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25 #include "../Framework/Inputs/TiledPyramidStatistics.h"
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26 #include "../Framework/Outputs/HierarchicalTiffWriter.h"
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28 #include <Core/Logging.h>
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29 #include <Core/OrthancException.h>
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30 #include <Plugins/Samples/Common/OrthancHttpConnection.h>
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32 #include "ApplicationToolbox.h"
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34
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35 static const char* OPTION_COLOR = "color";
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36 static const char* OPTION_HELP = "help";
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37 static const char* OPTION_INPUT = "input";
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38 static const char* OPTION_JPEG_QUALITY = "jpeg-quality";
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39 static const char* OPTION_OUTPUT = "output";
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40 static const char* OPTION_REENCODE = "reencode";
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41 static const char* OPTION_VERBOSE = "verbose";
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42 static const char* OPTION_VERSION = "version";
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43
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44 static bool ParseParameters(int& exitStatus,
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45 boost::program_options::variables_map& options,
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46 int argc,
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47 char* argv[])
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48 {
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49 // Declare the supported parameters
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50 boost::program_options::options_description generic("Generic options");
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51 generic.add_options()
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52 (OPTION_HELP, "Display this help and exit")
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53 (OPTION_VERSION, "Output version information and exit")
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54 (OPTION_VERBOSE, "Be verbose in logs")
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55 ;
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57 boost::program_options::options_description source("Options for the source DICOM image");
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58 source.add_options()
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59 ("orthanc", boost::program_options::value<std::string>()->default_value("http://localhost:8042/"),
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60 "URL to the REST API of the target Orthanc server")
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61 ;
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62 OrthancWSI::ApplicationToolbox::AddRestApiOptions(source);
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64 boost::program_options::options_description target("Options for the target TIFF image");
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65 target.add_options()
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66 (OPTION_COLOR, boost::program_options::value<std::string>(),
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67 "Color of the background for missing tiles (e.g. \"255,0,0\")")
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68 (OPTION_REENCODE, boost::program_options::value<bool>(),
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69 "Whether to re-encode each tile in JPEG (no transcoding, much slower) (Boolean)")
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70 (OPTION_JPEG_QUALITY, boost::program_options::value<int>(),
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71 "Set quality level for JPEG (0..100)")
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72 ;
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73
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74 boost::program_options::options_description hidden;
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75 hidden.add_options()
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76 (OPTION_INPUT, boost::program_options::value<std::string>(),
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77 "Orthanc identifier of the input series of interest")
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78 (OPTION_OUTPUT, boost::program_options::value<std::string>(),
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79 "Output TIFF file");
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80
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81 boost::program_options::options_description allWithoutHidden;
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82 allWithoutHidden.add(generic).add(source).add(target);
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83
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84 boost::program_options::options_description all = allWithoutHidden;
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85 all.add(hidden);
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86
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87 boost::program_options::positional_options_description positional;
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88 positional.add(OPTION_INPUT, 1);
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89 positional.add(OPTION_OUTPUT, 1);
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90
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91 bool error = false;
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92
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93 try
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94 {
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95 boost::program_options::store(boost::program_options::command_line_parser(argc, argv).
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96 options(all).positional(positional).run(), options);
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97 boost::program_options::notify(options);
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98 }
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99 catch (boost::program_options::error& e)
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100 {
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101 LOG(ERROR) << "Error while parsing the command-line arguments: " << e.what();
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102 error = true;
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103 }
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104
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105 if (!error &&
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106 options.count(OPTION_HELP) == 0 &&
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107 options.count(OPTION_VERSION) == 0)
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108 {
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109 if (options.count(OPTION_INPUT) != 1)
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110 {
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111 LOG(ERROR) << "No input series was specified";
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112 error = true;
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113 }
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114
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115 if (options.count(OPTION_OUTPUT) != 1)
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116 {
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117 LOG(ERROR) << "No output file was specified";
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118 error = true;
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119 }
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120 }
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121
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122 if (error || options.count(OPTION_HELP))
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123 {
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124 std::cout << std::endl
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125 << "Usage: " << argv[0] << " [OPTION]... [INPUT] [OUTPUT]"
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126 << std::endl
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127 << "Orthanc, lightweight, RESTful DICOM server for healthcare and medical research."
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128 << std::endl << std::endl
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129 << "Convert a DICOM image for digital pathology stored in some Orthanc server as a" << std::endl
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130 << "standard hierarchical TIFF (whose tiles are all encoded using JPEG)."
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131 << std::endl;
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132
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133 std::cout << allWithoutHidden << "\n";
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134
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135 if (error)
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136 {
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137 exitStatus = -1;
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138 }
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139
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140 return false;
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141 }
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142
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143 if (options.count(OPTION_VERSION))
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144 {
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145 OrthancWSI::ApplicationToolbox::PrintVersion(argv[0]);
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146 return false;
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147 }
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148
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149 if (options.count(OPTION_VERBOSE))
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150 {
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151 Orthanc::Logging::EnableInfoLevel(true);
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152 }
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153
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154 return true;
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155 }
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156
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157
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158
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159 static Orthanc::ImageAccessor* CreateEmptyTile(const OrthancWSI::IPyramidWriter& writer,
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160 const boost::program_options::variables_map& options)
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161 {
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162 std::auto_ptr<Orthanc::ImageAccessor> tile
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163 (OrthancWSI::ImageToolbox::Allocate(writer.GetPixelFormat(),
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164 writer.GetTileWidth(),
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165 writer.GetTileHeight()));
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166
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167 uint8_t red = 255;
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168 uint8_t green = 255;
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169 uint8_t blue = 255;
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170
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171 if (options.count(OPTION_COLOR))
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172 {
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173 OrthancWSI::ApplicationToolbox::ParseColor(red, green, blue, options[OPTION_COLOR].as<std::string>());
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174 }
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175
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176 OrthancWSI::ImageToolbox::Set(*tile, red, green, blue);
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177
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178 return tile.release();
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179 }
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180
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181
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182
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183 static void Run(OrthancWSI::ITiledPyramid& source,
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184 const boost::program_options::variables_map& options)
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185 {
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186 bool reencode = (options.count(OPTION_REENCODE) &&
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187 options[OPTION_REENCODE].as<bool>());
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188
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189 Orthanc::PhotometricInterpretation targetPhotometric;
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190
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191 if (reencode)
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192 {
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193 // The DicomToTiff tool only creates TIFF images with JPEG tiles (*)
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194 targetPhotometric = Orthanc::PhotometricInterpretation_YBRFull422;
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195 }
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196 else
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197 {
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198 targetPhotometric = source.GetPhotometricInterpretation();
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199 }
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200
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201 OrthancWSI::HierarchicalTiffWriter target(options[OPTION_OUTPUT].as<std::string>(),
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202 source.GetPixelFormat(),
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203 OrthancWSI::ImageCompression_Jpeg, // (*)
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204 source.GetTileWidth(),
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205 source.GetTileHeight(),
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206 targetPhotometric);
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207
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208 if (options.count(OPTION_JPEG_QUALITY))
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209 {
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210 target.SetJpegQuality(options[OPTION_JPEG_QUALITY].as<int>());
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211 }
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212
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213 LOG(WARNING) << "Source photometric interpretation: " << EnumerationToString(source.GetPhotometricInterpretation());
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214 LOG(WARNING) << "Target photometric interpretation: " << EnumerationToString(targetPhotometric);
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215
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216 std::auto_ptr<Orthanc::ImageAccessor> empty(CreateEmptyTile(target, options));
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217
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218 for (unsigned int level = 0; level < source.GetLevelCount(); level++)
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219 {
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220 LOG(WARNING) << "Creating level " << level << " of size "
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221 << source.GetLevelWidth(level) << "x" << source.GetLevelHeight(level);
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222 target.AddLevel(source.GetLevelWidth(level), source.GetLevelHeight(level));
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223 }
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224
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225 for (unsigned int level = 0; level < source.GetLevelCount(); level++)
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226 {
163
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227 LOG(WARNING) << std::string(reencode ? "Re-encoding" : "Transcoding")
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228 << " level " << level;
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229
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230 unsigned int countX = OrthancWSI::CeilingDivision
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231 (source.GetLevelWidth(level), source.GetTileWidth());
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232
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233 unsigned int countY = OrthancWSI::CeilingDivision
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234 (source.GetLevelHeight(level), source.GetTileHeight());
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235
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236 for (unsigned int tileY = 0; tileY < countY; tileY++)
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237 {
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238 for (unsigned int tileX = 0; tileX < countX; tileX++)
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239 {
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240 LOG(INFO) << "Dealing with tile (" << tileX << "," << tileY << ") at level " << level;
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241
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242 bool missing = false;
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243 bool success = true;
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244
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245 std::string tile;
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246 OrthancWSI::ImageCompression compression;
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247
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248 if (source.ReadRawTile(tile, compression, level, tileX, tileY))
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249 {
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250 if (compression == OrthancWSI::ImageCompression_Jpeg)
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251 {
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252 // Transcoding of JPEG tiles
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253 target.WriteRawTile(tile, compression, level, tileX, tileY);
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254 }
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255 else if (reencode)
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256 {
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257 std::auto_ptr<Orthanc::ImageAccessor> decoded;
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258
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259 if (compression == OrthancWSI::ImageCompression_None)
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260 {
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261 decoded.reset(OrthancWSI::ImageToolbox::DecodeRawTile(tile, source.GetPixelFormat(),
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262 source.GetTileWidth(), source.GetTileHeight()));
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263 }
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264 else
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265 {
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266 decoded.reset(OrthancWSI::ImageToolbox::DecodeTile(tile, compression));
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267 }
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268
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269 target.EncodeTile(*decoded, level, tileX, tileY);
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270 }
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271 else
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272 {
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273 success = false; // Re-encoding is mandatory
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274 }
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275 }
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276 else
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277 {
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278 // Unable to read the raw tile: The tile is missing (sparse tiling)
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279 missing = true;
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280 }
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281
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282 if (!success)
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283 {
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284 LOG(WARNING) << "Cannot transcode a DICOM image that is not encoded using JPEG (it is "
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285 << OrthancWSI::EnumerationToString(compression)
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286 << "), please use the --" << OPTION_REENCODE << "=1 option";
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287 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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288 }
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289
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290 if (missing)
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291 {
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292 LOG(WARNING) << "Sparse tiling: Using an empty image for missing tile ("
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293 << tileX << "," << tileY << ") at level " << level;
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294 target.EncodeTile(*empty, level, tileX, tileY);
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295 }
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296 }
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297 }
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298
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299 target.Flush();
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300 }
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301 }
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302
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303
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304
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305 int main(int argc, char* argv[])
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306 {
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307 OrthancWSI::ApplicationToolbox::GlobalInitialize();
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308 OrthancWSI::ApplicationToolbox::ShowVersionInLog(argv[0]);
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309
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310 int exitStatus = 0;
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311 boost::program_options::variables_map options;
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312
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313 try
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314 {
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315 if (ParseParameters(exitStatus, options, argc, argv))
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316 {
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317 Orthanc::WebServiceParameters params;
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318
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319 OrthancWSI::ApplicationToolbox::SetupRestApi(params, options);
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320
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321 OrthancPlugins::OrthancHttpConnection orthanc(params);
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322 OrthancWSI::DicomPyramid source(orthanc, options[OPTION_INPUT].as<std::string>(),
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323 false /* don't use cached metadata */);
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324
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325 OrthancWSI::TiledPyramidStatistics stats(source);
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326 Run(stats, options);
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327 }
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328 }
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329 catch (Orthanc::OrthancException& e)
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330 {
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331 LOG(ERROR) << "Terminating on exception: " << e.What();
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332
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333 if (options.count(OPTION_REENCODE) == 0)
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334 {
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335 LOG(ERROR) << "Consider using option \"--" << OPTION_REENCODE << "\"";
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336 }
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337
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338 exitStatus = -1;
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339 }
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340
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341 OrthancWSI::ApplicationToolbox::GlobalFinalize();
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342
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343 return exitStatus;
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344 }